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add oxygen tolerance

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dr. M.S. (Matthijs) Berends
2023-05-11 21:56:27 +02:00
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commit 91fa73dedf
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NEWS.md
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# AMR 2.0.0.9014
# AMR 2.0.0.9015
## Changed
* Added oxygen tolerance to over 25,000 bacteria in the `microorganisms` data set
* Added `mo_oxygen_tolerance()` to retrieve the values
* Added `mo_is_anaerobic()` to determine which species are obligate anaerobic bacteria
* Added LPSN and GBIF identifiers, and oxygen tolerance to `mo_info()`
* formatting fix for `sir_interpretation_history()`
* Fixed some WHONET codes for microorganisms and consequently a couple of entries in `clinical_breakpoints`
* Added microbial codes for Gram-negative/positive anaerobic bacteria
* `mo_rank()` now returns `NA` for 'unknown' microorganisms (`B_ANAER`, `B_ANAER-NEG`, `B_ANAER-POS`, `B_GRAMN`, `B_GRAMP`, `F_FUNGUS`, `F_YEAST`, and `UNKNOWN`)
* Fixed a bug for `as.mo()` that led to coercion of `NA` values when using custom microorganism codes
# AMR 2.0.0
This is a new major release of the AMR package, with great new additions but also some breaking changes for current users. These are all listed below.